This document is the thesis of Ang Chen submitted to the University of Geneva to obtain a Doctor of Science degree in computer science. The thesis proposes a multi-dimensional compositional approach for business process engineering using Concurrent Object-Oriented Petri Nets (CO-OPN). CO-OPN is a modeling language that can be used to model business processes and long-lasting transactional processes. It also allows generating prototypes from models. The thesis further presents ID-Net, an extension of Petri nets that supports data and encapsulation. ID-Net can be used to model complex systems in a modular way and its properties can be formally verified. Several case studies are discussed to demonstrate applying the proposed approaches to real-world problems